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opennotspecifiedAug 2023View details →

FIGURE 3 in Abelmoschus odishae (Malvoideae: Malvaceae): a new wild okra from tropical Eastern India

FIGURE 3. Abelmoschus odishae sp. nov. A. Habit: A1. Basal leaf, A2. Middle leaf, A3. Apical leaf; B. Stem with indumentum; C. Epicalyx: lateral view; D. Epicalyx: ventral view; E. Epicalyx enclosing flower bud; F. Longitudinal section of flower; G. Staminal column; H. Capsule; I. Seeds. Illustration by R.C.Misra.

opennotspecifiedAug 2023View details →

FIGURE 2 in Abelmoschus odishae (Malvoideae: Malvaceae): a new wild okra from tropical Eastern India

FIGURE 2. Abelmoschus odishae sp. nov. A–B. Stem and branch showing indumentum; C. Basal leaf; D. Middle leaf; E. Apical leaves; F. Epicalyx enclosing flower bud; G. Epicalyx: lateral view; H. Epicalyx: dorsal view; I. Flower: front view; J. L.S. of flower; K. Sepal; L. Petals; M. Staminal column with epicalyx and sepal; N. Fruit; O. Dehisced capsules; P. Seeds. Photographs by R.C.Misra.

opennotspecifiedAug 2023View details →

FIGURE 1 in Abelmoschus odishae (Malvoideae: Malvaceae): a new wild okra from tropical Eastern India

FIGURE 1. Abelmoschus odishae sp. nov. A. Natural occurrence of the species on a foot hill in Keonjhar district, Odisha; B. Location map of type collection site; C–D. Live plants maintained in the field gene bank; E. Type specimen preserved at ICAR-NBPGR, Cuttack. Photographs and location map by R.C.Misra.

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Data for: Genotypes selected for early and late avian lay date differ in their phenotype, but not fitness, in the wild

Global warming has shifted phenological traits in many species, but whether species are able to track further increasing temperatures depends on the fitness consequences of additional shifts in phenological traits. To test this, we conducted a genomic selection experiment on wild great tits from the Hoge Veluwe study population (The Netherlands) to obtain great tits (Parus major) with genotypes for extremely early and late egg lay dates and measured phenology and fitness of selected great tit females under wild conditions. Females with early genotypes advanced lay dates relative to females with late genotypes, but not relative to non-selected females. Females with early and late genotypes did not differ in the number of fledglings produced, in line with the weak effect of lay date on the number of fledglings produced by non-selected females in the years of the experiment. Our study is the first application of genomic selection in the wild and led to an asymmetric phenotypic response that indicates the presence of constraints toward early, but not late, lay dates.

opencc-zeroAug 2023View details →

Fig. 7 in Genome-wide identification and characterization of genes involved in melatonin biosynthesis in Morus notabilis (wild mulberry)

Fig. 7. Biosynthetic pathway of melatonin. The black arrows identify the pathway in herbaceous and woody plants while the red arrows identify the pathway in woody plants. The enzymes of the respective steps are as follows: TDC; T5H; SNAT; ASMT; and COMT. (For interpretation of the references to color in this figure legend, the reader is referred to the Web version of this article.)

Fig. 5 in Genome-wide identification and characterization of genes involved in melatonin biosynthesis in Morus notabilis (wild mulberry)

Fig. 5. Purification and enzymatic analyses of recombinant His-tagged MnASMT12. A: Purification of recombinant His-tagged MnASMT12 (lane1: Protein Marker; lane2: pCold TF (+IPTG); lane3: recombinant protein (-IPTG); lane4: recombinant protein (+IPTG); lane5: purified protein). B: Mass spectrum of compounds detected using UPLC-MS/MS. a: melatonin standard; b: Chromatogram of N-acetylserotonin catalyzed by MnASMT12. C: Determination of Km and Vmax of MnASMT12 for Nacetylserotonin. MnASMT12 (1.0 μg) was co-incubated with different concentrations of N-acetylserotonin for 20 min at 37 ◦C. D: Mass spectrum of compounds detected using UPLC-MS/MS. a: 5-methoxytryptamine standard; b: Chromatogram of serotonin catalyzed by MnASMT12. E: Determination of Km and Vmax of MnASMT12 for serotonin. MnASMT12 (1.0 μg) was co-incubated with different concentrations of serotonin for 20 min at 37 ◦C. " IPTG" stand without addition of 1 mM IPTG to the E. coli BL21 (DE3) culture, "+IPTG" stand addition of 1 mM IPTG to the E. coli BL21 (DE3) culture. "TF" is Trigger Factor, a prokaryotic ribosomerelated molecular chaperone that facilitates the translation and folding of peptides. "*" indicates Trigger factor.

Fig. 3 in Genome-wide identification and characterization of genes involved in melatonin biosynthesis in Morus notabilis (wild mulberry)

Fig. 3. Purification and enzymatic analyses of recombinant His-tagged MnTDC and recombinant His-tagged MnT5H2. A: Purification of recombinant His-tagged MnTDC (lane1: Protein Marker; lane2: pCold TF (+IPTG); lane3: recombinant protein (-IPTG); lane4: recombinant protein (+IPTG); lane5: purified protein). B: Mass spectrum of compounds detected using UPLC-MS/MS. a: tryptamine standard; b: Chromatogram of tryptophan catalyzed by MnTDC. C: Determination of Km and V of MnTDC for tryptophan. The MnTDC (1.0 μg) was co-incubated with different concentrations of tryptophan for 20 min at 37 ◦C. Trp: tryptophan; Try: max tryptamine. D: Purification of recombinant His-tagged MnT5H2 (lane1: Protein Marker; lane2: pCold TF (+IPTG); lane3: recombinant protein (-IPTG) lane4: recombinant protein (+IPTG); lane5: purified protein). E: Mass spectrum of compounds detected using UPLC-MS/MS. a: serotonin standard; b: Chromatogram of tryptamine catalyzed by MnT5H2. F: Determination of Km and Vmax of MnT5H2 for tryptamine. The MnT5H2 (1.0 μg) was co-incubated with different concentrations of tryptamine for 20 min at 28 ◦C. Ser: serotonin. " IPTG" stand without addition of 1 mM IPTG to the E. coli BL21 (DE3) culture, "+IPTG" stand addition of 1 mM IPTG to the E. coli BL21 (DE3) culture. "TF" is Trigger Factor, a prokaryotic ribosome-related molecular chaperone that facilitates the translation and folding of peptides. "*" indicates Trigger factor.

Fig. 4 in Genome-wide identification and characterization of genes involved in melatonin biosynthesis in Morus notabilis (wild mulberry)

Fig. 4. Purification and enzymatic analyses of recombinant His-tagged MnSNAT5. A: Purification of recombinant His-tagged MnSNAT5 (lane1: Protein Marker; lane2: pCold TF (+IPTG); lane3: recombinant (-IPTG); lane4: recombinant (+IPTG); lane5: purified protein). B: Mass spectrum of compounds detected using UPLCMS/MS. a: N-acetylserotonin standard; b: Chromatogram of serotonin catalyzed by MnSNAT5. C: Determination of Km and Vmax of MnSNAT5 for serotonin. MnSNAT5 (1.0 μg) was co-incubated with different concentrations of serotonin for 20 min at 37 ◦C. D: Mass spectrum of compounds detected using UPLC-MS/MS. a: standard, b: Chromatogram of 5-methoxytryptamine catalyzed by MnSNAT5. E: Determination of Km and Vmax of MnSNAT5 for 5-methoxytryptamine. MnSNAT5 (1.0 μg) was coincubated with different concentrations of 5-methoxytryptamine for 20 min at 37 ◦C. " IPTG" stand without addition of 1 mM IPTG to the E. coli BL21 (DE3) culture, "+IPTG" stand addition of 1 mM IPTG to the E. coli BL21 (DE3) culture. "TF" is Trigger Factor, a prokaryotic ribosome-related molecular chaperone that facilitates the translation and folding of peptides. "*" indicates Trigger factor. NAS: N-acetylserotonin; 5-MT: 5-methoxytryptamine; Mel: melatonin.

Fig. 2 in Genome-wide identification and characterization of genes involved in melatonin biosynthesis in Morus notabilis (wild mulberry)

Fig. 2. Expression analysis of genes involved in melatonin biosynthesis. A: Heat map showing tissue-specific expression profiles of melatonin biosynthetic genes in M. notabilis, including MnTDC, MnT5Hs, MnSNATs, MnASMT genes and MnCOMTs. Sample names are shown above the heat maps. The color scale indicates the degree of expression: "green" indicates low expression; "red" indicates high expression. B: Tissue-specific expression levels of MnTDC, MnT5H2, MnSNAT5, MnASMT12 and MnCOMT1 as determined by qRT-PCR. Data was analyzed using 2 ΔCt method and MnACTIN3 was used as an internal control. Data are means ±SDs (n = 3), significant differences (P <0.05) are indicated by different letters above the bars. (For interpretation of the references to color in this figure legend, the reader is referred to the Web version of this article.)

Fig. 1 in Genome-wide identification and characterization of genes involved in melatonin biosynthesis in Morus notabilis (wild mulberry)

Fig. 1. Phylogenetic tree of amino acid sequences of genes involved in melatonin biosynthesis in M. notabilis and other plants. The phylogenetic trees were generated with the neighbor-joining method using MEGA 5.0 software. All IDs of gene in other plant species involved in melatonin biosynthesis are provided in Supplementary Table S1. Red circles: M. notabilis genes. A, TDC; B, T5H; C, SNAT; D, ASMT. ASMT proteins were separated into three classes: I (black), II (red), III (blue); E, COMT. (For interpretation of the references to color in this figure legend, the reader is referred to the Web version of this article.)

opennotspecifiedOct 2021View details →

Fig. 3 in Authenticating wild Piper species (peppers) originating from islands in the Indian Ocean on the basis of morphological, genetic and chemical characteristics

Fig. 3. Phylogenetic dendrogram obtained from the combined sequences (Its + psbJ-petA) using the Neighbour Joining (NJ) method.

opencc-by-4.0Aug 2023View details →

Repeatome turnover meets stable chromosomes: repetitive DNA sequences mark speciation and gene pool boundaries in sugar beet and wild beets

The present repository provides zipped archives containing the results of the RepeatExplorer2 runs of individual as well as comparative repeat analyses in beet genomes.   Sugar beet (Beta vulgaris subsp. vulgaris) and its crop wild relatives share a base chromosome number of nine and similar chromosome morphologies. Yet, interspecific breeding is impeded by chromosome and sequence divergence that is still not fully understood. Since repetitive DNA sequences represent the fastest evolving parts of the genome, they likely impact genomic variability and contribute to the separation of beet gene pools. Hence, we investigated if innovations and losses in the repeatome can be linked to chromosomal differentiation and speciation. We traced genome- and chromosome-wide evolution across sugar beet and twelve wild beets comprising all sections of the beet genera Beta and Patellifolia. For this, we combined data from short and long read sequencing, flow cytometry, and cytogenetics to build a comprehensive data framework for our beet panel that spans the complete scale from DNA sequence to chromosome up to the genome. Genome sizes and repeat profiles reflect the separation of the beet species into three gene pools. These gene pools harbor repeats with contrasting evolutionary patterns: We identified section- and species-specific repeat emergences and losses, e.g. of the retrotransposons causal for genome expansions in the section Corollinae/Nanae. Since most genomic variability was found in the satellite DNAs, we focused on tracing the 19 beetSat families across the three beet sections/genera. These taxa harbor evidence for contrasting strategies in repeat evolution, leading to contrasting satellite DNA profiles and fundamentally different centromere architectures, ranging from chromosomal uniformity in Beta and Patellifolia species to the formation of patchwork chromosomes in Corollinae/Nanae species.  We show that repetitive DNA sequences are causal for genome size expansion and contraction across the beet genera, providing insights into the genomic underpinnings of beet speciation. Satellite DNAs in particular vary considerably among beet taxa, leading to the evolution of distinct chromosomal setups. These differences likely contribute to the barriers in beet breeding between the three gene pools. Thus, with their isokaryotypic chromosome sets, beet genomes present an ideal system for studying the link between repeats, genome variability, and chromosomal differentiation/evolution and provide a theoretical basis for understanding barriers in crop breeding.

Fig. 4 in Glandular trichome-derived sesquiterpenes of wild tomato accessions (Solanum habrochaites) affect aphid performance and feeding behavior

Fig. 4. Effect of pure β-caryophyllene and α-humulene on M. euphorbiae feeding performance (A–C) and choice behavior (D). Different amounts of a mix of pure β-caryophyllene and α-humulene (3:1 ratio) were added to the feeding diet. The data in (A), (B), and (C) show the comparison of Kaplan-Meier survival curves (logrank test, α =0.05), gel saliva density (Tukey's HSD, α =0.05), and number of honeydew drops (ANOVA, α = 0.05), respectively, upon addition of different amounts of pure sesquiterpenes to the artificial diet. The data in (D) represent the behavioral responses of aphid alatae to odors from leaves of c.v. M82 alone (right bars) or from leaves of c.v. M82 leaves in combination with different amounts of a mix of pure β-caryophyllene and α-humulene (left bars) (Chi-square goodness of fit; *, P <0.05; **, P <0.01).

Fig. 5 in Glandular trichome-derived sesquiterpenes of wild tomato accessions (Solanum habrochaites) affect aphid performance and feeding behavior

Fig. 5. α-Santalene and α-bergamotene producing tomato introgression line affects performance, feeding and choice behavior of M. euphorbiae. (A) Performance of M. euphorbiae apterae arrested on the leaf surface of S. lycopersicum LA4024, S. habrochaites LA1777, and the introgression lines LA3935, LA3934, LA3936, and LA3937. Values for longevity and fecundity are presented as mean ± SE and compared by Tukey's HSD test (α =0.05). (B) Kaplan-Meier estimates of survivorship of M. euphorbiae apterae feeding on artificial diets containing leaf dip extracts of S. lycopersicum LA4024, S. habrochaites LA1777, and the introgression line LA3935 (logrank test, α = 0.05). (C) and (D) Box plots represent means ± SE of gel saliva density (cm 2) and number of honeydew drops, respectively. Tukey's HSD tests (α = 0.05) are used for post-hoc analysis. (E) Choice of M. euphorbiae alatae between odors from LA4024 leaves alone (left bars) and from LA4024 leaves with added leaf dip extracts (100 and 300 μL) from the introgression line LA3935 or S. habrochaites LA1777 (right bars) (Chi-square goodness of fit; *, P <0.05; **, P <0.01).

Fig. 3 in Glandular trichome-derived sesquiterpenes of wild tomato accessions (Solanum habrochaites) affect aphid performance and feeding behavior

Fig. 3. Choice behavior of M. euphorbiae alatae in an open Y-track olfactometer. (A) Choice of aphids between air and odors from leaves of different S. lycopersicum cultivars or S. habrochaites accessions. (B) Choice of aphids between odors from leaves of c.v. M82 and different S. habrochaites accessions. (C) Choice of aphids between odors from leaves of c.v. M82 leaves alone (left bars) and from leaves of c.v. M82 leaves with added S. habrochaites leaf dip extracts (right bars). Asterisks following each pair of bars indicates significant differences according to Chi-square goodness of fit (⋅, P <0.07; *, P <0.05; **, P <0.01).

Fig. 2 in Glandular trichome-derived sesquiterpenes of wild tomato accessions (Solanum habrochaites) affect aphid performance and feeding behavior

Fig. 2. Feeding performance of M. euphorbiae apterae on artificial diets containing leaf dip extracts of S. lycopersicum c.v. M82 and different S. habrochaites accessions (MTBE solvent control). (A) Kaplan-Meier estimates of survivorship and analysis of log-rank test (α =0.05). (B) Box and violin plots represent mean ± SE of gel saliva density (cm 2) and the probability density, respectively. (C) Number of honeydew drops accumulated in the feeding chambers. Asterisks in (B) and (C) represent significant differences between diets with leaf dip extracts and control based on Dunnett's test (⋅, P <0.08; *, P <0.05; **, P <0.01; ***, P <0.001).

Fig. 1 in Glandular trichome-derived sesquiterpenes of wild tomato accessions (Solanum habrochaites) affect aphid performance and feeding behavior

Fig. 1. Longevity (A) and fecundity (B) of M. euphorbiae apterae arrested on the leaf surface of two S. lycopersicum cultivars and different S. habrochaites accessions. Solanum habrochaites accessions represent five chemotypes characterized by the production of different sesquiterpenes in their glandular trichomes. Values for longevity and fecundity are presented as mean ± SE. Different letters indicate that logarithmic values were significantly different (Tukey's HSD test, α = 0.05).

Fig. 1 in Natural variation of diterpenoid phytoalexins in cultivated and wild rice species

Fig. 1. Accumulation of momilactones A and B in cultivars from the WRC and wild rice species after UV irradiation. (A) Momilactone A amounts in WRC cultivars. (B) Momilactone B amounts in WRC cultivars. (C) Correlation between the amounts of momilactones A and B. R2: decision coefficient. (D) Amounts of momilactones A and B in wild rice species. Or-I, Or-II, and Or-III indicate clades of O. rufipogon. O. gla: O. glaberrima; O. bar: O. barthii; O. glu: O. glumaepatula; O. mer: O. meridionalis; O. pun: O. punctata; O. bra: O. brachyantha. Values are means ± SD of three biological replicates. n.d.: not detected.

Fig. 2 in Natural variation of diterpenoid phytoalexins in cultivated and wild rice species

Fig. 2. Accumulation of phytocassanes A and D in cultivars from the WRC and wild rice species after UV irradiation. (A) Phytocassane A amounts in WRC cultivars. (B) Phytocassane D amounts in WRC cultivars. (C) Correlation between amounts of phytocassanes A and D. R 2: decision coefficient. (D) Amounts of phytocassanes A and D in wild rice species. Or-I, Or-II, and Or-III indicate clades of O. rufipogon. O. gla: O. glaberrima; O. bar: O. barthii; O. glu: O. glumaepatula; O. mer: O. meridionalis; O. pun: O. punctata; O. bra: O. brachyantha. Values are means ± SD of three biological replicates. n.d.: not detected.

Fig. 5 in Natural variation of diterpenoid phytoalexins in cultivated and wild rice species

Fig. 5. Analysis of the chemical structure of 2. (A) COSY (bold lines) and HMBC (black arrows from protons to carbon atoms) correlations of 2. (B) Chemical structure of phytocassane A. (C) NOESY correlations on the three-dimensional chemical structure of 2. (D) Chemical structure of 2.